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Ji H, Sandstrom P. Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing. Pathogens 2022; 11:pathogens11070739. [PMID: 35889985 PMCID: PMC9321895 DOI: 10.3390/pathogens11070739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
The close monitoring of HIV drug resistance using genotypic HIV drug resistance testing (HIVDRT) has become essential for effective HIV/AIDS management at both individual and population levels. Over the years, a broad spectrum of analytes or specimens have been applied or attempted in HIVDRT; however, the suitability and performance of these analytes in HIVDRT and the clinical relevance of the results from them may vary significantly. This article provides a focused overview of the performance, strengths, and weaknesses of various analytes while used in HIVDRT, which may inform the optimal analytes selection in different application contexts.
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Affiliation(s)
- Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-789-6521
| | - Paul Sandstrom
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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2
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Abstract
The use of saliva as a diagnostic biofluid has been increasing in recent years, thanks to the identification and validation of new biomarkers and improvements in test accuracy, sensitivity, and precision that enable the development of new noninvasive and cost-effective devices. However, the lack of standardized methods for sample collection, treatment, and storage contribute to the overall variability and lack of reproducibility across analytical evaluations. Furthermore, the instability of salivary biomarkers after sample collection hinders their translation into commercially available technologies for noninvasive monitoring of saliva in home settings. The present review aims to highlight the status of research on the challenges of collecting and using diagnostic salivary samples, emphasizing the methodologies used to preserve relevant proteins, hormones, genomic, and transcriptomic biomarkers during sample handling and analysis.
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Affiliation(s)
- Luciana d'Amone
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Giusy Matzeu
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States
| | - Fiorenzo G Omenetto
- Silklab, Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Electrical and Computer Engineering, Tufts University, Medford, Massachusetts 02155, United States.,Department of Physics, Tufts University, Medford, Massachusetts 02155, United States.,Laboratory for Living Devices, Tufts University, Medford, Massachusetts 02155, United States
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Hans L, Marins EG, Simon CO, Magubane D, Seiverth B, Carmona S. Classification of HIV-1 virological treatment failure using the Roche cobas plasma separation card on cobas 8800 compared to dried blood spots on Abbott RealTime HIV-1. J Clin Virol 2021; 140:104839. [PMID: 33991979 DOI: 10.1016/j.jcv.2021.104839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Measurement of HIV-1 viral load (VL) is essential for monitoring antiretroviral treatment (ART) efficacy. In remote settings, dried blood spots (DBS) may be used as the specimen type. However, cellular components in DBS not present in the gold standard specimen type, plasma, may result in low specificity i.e., over-estimation of VL results from DBS compared to plasma. The Abbott RealTime HIV-1 assay system has been reported to have improved specificity using DBS compared to other tests. A new specimen collection matrix, the cobas plasma separation card (PSC, Roche Molecular Systems), enables specimen collection from a finger prick or venous blood, using a multi-layer absorption and filtration design that results in a specimen similar to plasma. OBJECTIVES AND STUDY DESIGN We performed a direct comparison between VL results from PSC tested with the cobas 6800/8800 assay (c8800) and DBS tested with the Abbott RealTime HIV-1 assay. RESULTS Overall concordance between PSC and plasma around the 1000 copies/mL threshold was high (>97%). Compared to VL measured using DBS and the RealTime assay, PSC and c8800 showed improved sensitivity (96.9% vs 90.6%) and specificity (97.4% vs. 87.2%) using plasma as the reference, as there were fewer patients with VL below 1000 copies/mL in plasma in whom VL was over this threshold using PSC compared to DBS. The limit of detection for PSC was lower than for DBS (575 vs. 2314 copies/mL). CONCLUSIONS cobas PSC represents a promising specimen type for use with the cobas 6600/8800 system in settings where plasma cannot be used.
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Affiliation(s)
- Lucia Hans
- University of the Witwatersrand, School of Pathology, Department of Molecular Medicine and Haematology, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa.
| | - Ed G Marins
- Roche Molecular Systems, Inc., Pleasanton, United States
| | | | - Dieketseng Magubane
- University of the Witwatersrand, School of Pathology, Department of Molecular Medicine and Haematology, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
| | | | - Sergio Carmona
- University of the Witwatersrand, School of Pathology, Department of Molecular Medicine and Haematology, Johannesburg, South Africa; National Health Laboratory Service, Johannesburg, South Africa
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Park SL, Huang YJS, Higgs S, Vanlandingham DL. Application of a Nonpaper Based Matrix to Preserve Chikungunya Virus Infectivity at Ambient Temperature. Vector Borne Zoonotic Dis 2018; 18:278-281. [PMID: 29652645 DOI: 10.1089/vbz.2017.2212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
For over 100 years, field studies on arboviruses and the subsequent delivery and administration of live attenuated vaccines have been complicated by the need to maintain a so-called "cold chain," which is the source to destination refrigeration of biological materials. In this study we describe the application of a nonpaper based matrix and demonstrate preservation of chikungunya virus infectivity at ambient temperature for 7 days. The technique was successfully employed using infectious cell culture medium and infected mosquito homogenate samples. This technique provides a simple solution for conducting studies in resource-limited areas, where the maintenance of a cold chain is technically challenging.
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Affiliation(s)
- So Lee Park
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas.,2 Biosecurity Research Institute, Kansas State University , Manhattan, Kansas
| | - Yan-Jang S Huang
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas.,2 Biosecurity Research Institute, Kansas State University , Manhattan, Kansas
| | - Stephen Higgs
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas.,2 Biosecurity Research Institute, Kansas State University , Manhattan, Kansas
| | - Dana L Vanlandingham
- 1 Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University , Manhattan, Kansas.,2 Biosecurity Research Institute, Kansas State University , Manhattan, Kansas
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Levine M, Beck I, Styrchak S, Pepper G, Frenkel L. Comparison of Matrix-Based and Filter Paper-Based Systems for Transport of Plasma for HIV-1 RNA Quantification and Amplicon Preparation for Genotyping. J Clin Microbiol 2016; 54:1899-1901. [PMID: 27076660 PMCID: PMC4922083 DOI: 10.1128/jcm.00541-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 04/08/2016] [Indexed: 11/20/2022] Open
Abstract
Two ambient-temperature, dry plasma transport systems, ViveST tubes and RNASound RNA sampling cards, and two extraction methods were compared to frozen plasma for HIV-1 RNA recovery. Significant RNA loss occurred: ViveST+MiniMag > ViveST+QIAamp > RNASound+QIAamp. RNA loss and low specimen volumes may affect the sensitivity of genotyping specimens with HIV-1 RNA of <4.70 log10 copies/ml.
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Affiliation(s)
- Molly Levine
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Ingrid Beck
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Sheila Styrchak
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | | | - Lisa Frenkel
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
- University of Washington, Seattle, Washington, USA
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Dauner AL, Gilliland TC, Mitra I, Pal S, Morrison AC, Hontz RD, Wu SJL. Evaluation of nucleic acid stabilization products for ambient temperature shipping and storage of viral RNA and antibody in a dried whole blood format. Am J Trop Med Hyg 2015; 93:46-53. [PMID: 25940193 PMCID: PMC4497903 DOI: 10.4269/ajtmh.15-0110] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 03/24/2015] [Indexed: 11/07/2022] Open
Abstract
Loss of sample integrity during specimen transport can lead to false-negative diagnostic results. In an effort to improve upon the status quo, we used dengue as a model RNA virus to evaluate the stabilization of RNA and antibodies in three commercially available sample stabilization products: Whatman FTA Micro Cards (GE Healthcare Life Sciences, Pittsburgh, PA), DNAstāble Blood tubes (Biomātrica, San Diego, CA), and ViveST tubes (ViveBio, Alpharetta, GA). Both contrived and clinical dengue-positive specimens were stored on these products at ambient temperature or 37°C for up to 1 month. Antibody and viral RNA levels were measured by enzyme-linked immunosorbent assay (ELISA) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays, respectively, and compared with frozen unloaded controls. We observed reduced RNA and antibody levels between stabilized contrived samples and frozen controls at our earliest time point, and this was particularly pronounced for the FTA cards. However, despite some time and temperature dependent loss, a 94.6-97.3% agreement was observed between stabilized clinical specimens and their frozen controls for all products. Additional considerations such as cost, sample volume, matrix, and ease of use should inform any decision to incorporate sample stabilization products into a diagnostic testing workflow. We conclude that DNAstāble Blood and ViveST tubes are useful alternatives to traditional filter paper for ambient temperature shipment of clinical specimens for downstream molecular and serological testing.
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Affiliation(s)
| | | | | | - Subhamoy Pal
- *Address correspondence to Subhamoy Pal, Viral and Rickettsial Diseases Department, Naval Medical Research Center, Building 17, Suite 2B, NSA Bethesda, MD 20889. E-mail:
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Monitoring the quality of HIV-1 viral load testing through a proficiency testing program using dried tube specimens in resource-limited settings. J Clin Microbiol 2015; 53:1129-36. [PMID: 25609733 DOI: 10.1128/jcm.02780-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 viral load (VL) levels are used for monitoring disease progression and antiretroviral therapy outcomes in HIV-infected patients. To assess the performance of laboratories conducting HIV-1 VL testing in resource-limited settings, the U.S. Centers for Disease Control and Prevention implemented a voluntary, free-of-charge, external quality assurance program using dried tube specimens (DTSs). Between 2010 and 2012, DTS proficiency testing (PT) panels consisting of 5 specimens were distributed at ambient temperature to participants. The results from the participants (n≥6) using the same assay were grouped, analyzed, and graded as acceptable within a group mean±3 standard deviations. Mean proficiency scores were calculated by dividing the combined PT scores by the number of testing cycles using a linear regression model. Between 2010 and 2012, the number of participants enrolled increased from 32 in 16 countries to 114 in 44 countries. A total of 78.2% of the participants reported results using 10 different VL assays. The rates of reporting of acceptable results by the participants were 96.6% for the Abbott assay, 96.3% for the Roche Cobas assay, 94.5% for the Roche Amplicor assay, 93.0% for the Biocentric assay, and 89.3% for the NucliSens assay. The overall mean proficiency scores improved over time (P=0.024). DTSs are a good alternative specimen type to plasma specimens for VL PT programs, as they do not require cold chain transportation and can be used on PCR-based assays. Our data suggest that the CDC HIV-1 VL PT program using DTSs positively impacts the testing performance of the participants, which might translate into better and more accurate VL testing services for patients.
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HIV diversity and drug resistance from plasma and non-plasma analytes in a large treatment programme in western Kenya. J Int AIDS Soc 2014; 17:19262. [PMID: 25413893 PMCID: PMC4238965 DOI: 10.7448/ias.17.1.19262] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 09/23/2014] [Accepted: 10/10/2014] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Antiretroviral resistance leads to treatment failure and resistance transmission. Resistance data in western Kenya are limited. Collection of non-plasma analytes may provide additional resistance information. METHODS We assessed HIV diversity using the REGA tool, transmitted resistance by the WHO mutation list and acquired resistance upon first-line failure by the IAS-USA mutation list, at the Academic Model Providing Access to Healthcare (AMPATH), a major treatment programme in western Kenya. Plasma and four non-plasma analytes, dried blood-spots (DBS), dried plasma-spots (DPS), ViveST(TM)-plasma (STP) and ViveST-blood (STB), were compared to identify diversity and evaluate sequence concordance. RESULTS Among 122 patients, 62 were treatment-naïve and 60 treatment-experienced; 61% were female, median age 35 years, median CD4 182 cells/µL, median viral-load 4.6 log10 copies/mL. One hundred and ninety-six sequences were available for 107/122 (88%) patients, 58/62 (94%) treatment-naïve and 49/60 (82%) treated; 100/122 (82%) plasma, 37/78 (47%) attempted DBS, 16/45 (36%) attempted DPS, 14/44 (32%) attempted STP from fresh plasma and 23/34 (68%) from frozen plasma, and 5/42 (12%) attempted STB. Plasma and DBS genotyping success increased at higher VL and shorter shipment-to-genotyping time. Main subtypes were A (62%), D (15%) and C (6%). Transmitted resistance was found in 1.8% of plasma sequences, and 7% combining analytes. Plasma resistance mutations were identified in 91% of treated patients, 76% NRTI, 91% NNRTI; 76% dual-class; 60% with intermediate-high predicted resistance to future treatment options; with novel mutation co-occurrence patterns. Nearly 88% of plasma mutations were identified in DBS, 89% in DPS and 94% in STP. Of 23 discordant mutations, 92% in plasma and 60% in non-plasma analytes were mixtures. Mean whole-sequence discordance from frozen plasma reference was 1.1% for plasma-DBS, 1.2% plasma-DPS, 2.0% plasma-STP and 2.3% plasma-STB. Of 23 plasma-STP discordances, one mutation was identified in plasma and 22 in STP (p<0.05). Discordance was inversely significantly related to VL for DBS. CONCLUSIONS In a large treatment programme in western Kenya, we report high HIV-1 subtype diversity; low plasma transmitted resistance, increasing when multiple analytes were combined; and high-acquired resistance with unique mutation patterns. Resistance surveillance may be augmented by using non-plasma analytes for lower-cost genotyping in resource-limited settings.
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Diallo K, Lehotzky E, Zhang J, Zhou Z, de Rivera IL, Murillo WE, Nkengasong J, Sabatier J, Zhang G, Yang C. Evaluation of a dried blood and plasma collection device, SampleTanker(®), for HIV type 1 drug resistance genotyping in patients receiving antiretroviral therapy. AIDS Res Hum Retroviruses 2014; 30:67-73. [PMID: 23944768 DOI: 10.1089/aid.2013.0127] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Whatman 903 filter paper is the only filter paper that has been used for HIV drug resistance (HIVDR) genotyping in resource-limited settings. In this study, we evaluated another dried blood specimen collection device, termed SampleTanker(®) (ST), for HIVDR genotyping. Blood specimens from 123 antiretroviral therapy (ART)-experienced patients were used to prepare ST whole blood and ST plasma specimens; they were then stored at ambient temperature for 2 or 4 weeks. The remaining plasma specimens were stored at -80°C and used as frozen plasma controls. Frozen plasma viral load (VL) was determined using the Roche Amplicor HIV-1 Monitor test, v.1.5 and 50 specimens with VL ≥3.00 log10 copies/ml were genotyped using the broadly sensitive genotyping assay. The medium VL for the 50 frozen plasma specimens with VL ≥3.00 log10 was 3.58 log10 copies/ml (IQR: 3.32-4.11) and 96.0% (48/50) of them were genotyped. Comparing to frozen plasma specimens, significantly lower genotyping rates were obtained from ST whole blood (48.98% and 42.85%) and ST plasma specimens (36.0% and 36.0%) stored at ambient temperature for 2 and 4 weeks, respectively (p<0.001). Nucleotide sequence identity and resistance profile analyses between the matched frozen plasma and ST whole blood or ST plasma specimens revealed high nucleotide sequence identities and concordant resistance profiles (98.1% and 99.0%, and 96.6% and 98.9%, respectively). Our results indicate that with the current design, the ST may not be the ideal dried blood specimen collection device for HIVDR monitoring for ART patients in resource-limited settings.
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Affiliation(s)
- Karidia Diallo
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Erica Lehotzky
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jing Zhang
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Zhiyong Zhou
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Wendy E. Murillo
- National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - John Nkengasong
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer Sabatier
- Strategic Information and Epidemiology Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Guoqing Zhang
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Chunfu Yang
- International Laboratory Branch, Division of Global HIV/AIDS, CGH, Centers for Disease Control and Prevention, Atlanta, Georgia
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Investigating the use of protein saver cards for storage and subsequent detection of bovine anti-Brucella abortus smooth lipopolysaccharide antibodies and gamma interferon. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2013; 20:1669-74. [PMID: 23986318 DOI: 10.1128/cvi.00033-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Brucella abortus, a smooth strain of the genus Brucella, is the causative agent of bovine brucellosis. To support the ongoing development of diagnostic tests for bovine brucellosis, the use of Protein Saver cards (Whatman) for bovine blood serum and plasma sample collection has been evaluated. These cards offer significant logistical and safety alternatives to transporting and storing liquid samples and may aid in diagnostic programs and validation studies. To evaluate the utility of these cards, 204 bovine blood serum samples from Brucella-infected and noninfected animals were stored on and eluted from the Protein Saver cards. Anti-Brucella smooth lipopolysaccharide (sLPS) antibody titers for the serum eluates were compared to those of the unprocessed original serum samples by indirect enzyme-linked immunosorbent assay (ELISA). The results showed a highly significant correlation between titers from the serum eluates and the unprocessed sera. Therefore, under these circumstances, serum eluates and unprocessed serum samples may be used interchangeably. Blood plasma from 113 mitogen-stimulated whole-blood samples was added to and eluted from the Protein Saver cards. The gamma interferon (IFN-γ) titers in the plasma eluates were compared to those of the unprocessed plasma samples obtained by IFN-γ ELISA. The results showed a significant correlation between the plasma eluates and the unprocessed plasma samples. To derive a signal in the plasma eluate, it was necessary to develop a novel and highly sensitive ELISA for the detection of IFN-γ. The serum samples stored on cards at room temperature over a 10-day period showed little variation in antibody titers. However, the plasma eluates showed a progressive loss of IFN-γ recovery over 10 days when stored at room temperature.
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Barr KL, Messenger AM, Anderson BD, Friary JA, Heil GL, Reece K, Gray GC. Recovery of live virus after storage at ambient temperature using ViveST™. J Clin Virol 2012; 56:57-61. [PMID: 23046621 DOI: 10.1016/j.jcv.2012.09.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 09/11/2012] [Accepted: 09/13/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND A major impediment to performing virological field studies in developing nations is the lack of ultra-low freezers as well as the expense and difficulty of shipping frozen samples. A commercially available product, ViveST™, was developed to preserve nucleic acids at ambient temperature for use in specimen storage and transportation. However, its applications as a viral storage, transport and recovery device have not been evaluated. OBJECTIVE To examine the ability of ViveST to preserve live virus following storage at ambient temperature. STUDY DESIGN A panel of six viruses was stored at ambient temperature (~22°C) in ViveST with fetal bovine serum (FBS), or ViveST with minimal essential media (MEM) and compared with virus stored in universal transport media (M4RT), MEM, and FBS alone. Stored viruses included: human adenovirus (14p), dengue virus 2 (16608), echovirus 3 (Morrisey), human rhinovirus 15 (1734), Coxsackie virus B5 (Faulkner), and herpes simplex virus 1 (HF). After 7 days storage at ambient temperature, virus recovery was measured via titration using viral plaque assays or focus-forming unit assays. RESULTS Viral titer studies indicate that ViveST with either FBS or M4RT preserved/recovered 5 different viruses for 1 week at ambient temperature. MEM preserved 4 viruses while FBS and ViveST with MEM preserved 3 viruses each. Statistical analyses indicate that M4RT and ViveST with FBS preserved significantly more virus than the other treatments. CONCLUSIONS These data suggest that ViveST with either FBS or M4RT may be useful in field specimen collection scenarios where ultra-cold storage is not available.
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Affiliation(s)
- Kelli L Barr
- College of Public Health and Health Professions and The Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States.
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Stevens DS, Crudder CH, Domingo GJ. Post-extraction stabilization of HIV viral RNA for quantitative molecular tests. J Virol Methods 2012; 182:104-10. [PMID: 22433512 DOI: 10.1016/j.jviromet.2012.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 02/13/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022]
Abstract
Two approaches to stabilize viral nucleic acid in processed clinical specimens were evaluated. HIV-1 RNA extracted from clinical specimens was stabilized in a dry matrix in a commercial product (RNAstable, Biomatrica, San Diego, CA, USA) and in a reverse-transcription reaction mixture in liquid form as cDNA. As few as 145 HIV-1 genome copies of viral RNA are reliably stabilized by RNAstable at 45°C for 92 days and in the cDNA format at 45°C for 7 days as determined by real-time PCR. With RNAstable the R(2) at days 1, 7, and 92 were 0.888, 0.871, and 0.943 when compared to baseline viral load values. The cDNA generated from the same clinical specimens was highly stable with an R(2) value of 0.762 when comparing viral load determinations at day 7 to baseline values. In conclusion viral RNA stabilized in a dry RNAstable matrix is highly stable for long periods of time at high temperatures across a substantial dynamic range. Viral RNA signal can also be stabilized in liquid in the form of cDNA for limited periods of time. Methods that reduce reliance on the cold chain and preserve specimen integrity are critical for extending the reach of molecular testing to low-resource settings. Products based on anhydrobiosis, such as the RNAstable should be evaluated further to support viral pathogen diagnosis.
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Santos C, Reis A, dos Santos CV, Damas C, Silva MH, Viana MV, Ferraz ML, Carnauba D, El-Far F, Serra F, Diaz RS. The use of real-time PCR to detect hepatitis C virus RNA in dried blood spots from Brazilian patients infected chronically. J Virol Methods 2012; 179:17-20. [DOI: 10.1016/j.jviromet.2011.06.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 06/08/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
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Balakrishnan P, Iqbal HS, Shanmugham S, Mohanakrishnan J, Solomon SS, Mayer KH, Solomon S. Low-cost assays for monitoring HIV infected individuals in resource-limited settings. Indian J Med Res 2011; 134:823-34. [PMID: 22310816 PMCID: PMC3284092 DOI: 10.4103/0971-5916.92628] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Indexed: 11/23/2022] Open
Abstract
Use of a combination of CD4 counts and HIV viral load testing in the management of antiretroviral therapy (ART) provides higher prognostic estimation of the risk of disease progression than does the use of either test alone. The standard methods to monitor HIV infection are flow cytometry based for CD4+ T cell count and molecular assays to quantify plasma viral load of HIV. Commercial assays have been routinely used in developed countries to monitor ART. However, these assays require expensive equipment and reagents, well trained operators, and established laboratory infrastructure. These requirements restrict their use in resource-limited settings where people are most afflicted with the HIV-1 epidemic. With the advent of low-cost and/or low-tech alternatives, the possibility of implementing CD4 count and viral load testing in the management of ART in resource-limited settings is increasing. However, an appropriate validation should have been done before putting them to use for patient testing.
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Affiliation(s)
- Pachamuthu Balakrishnan
- YRG Centre for AIDS Research & Education, Voluntary Health Services, Taramani, Chennai, India.
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Comparative effectiveness of dried-plasma hepatitis B virus viral load (VL) testing in three different VL commercial platforms using ViveST for sample collection. J Clin Microbiol 2011; 50:145-7. [PMID: 22012021 DOI: 10.1128/jcm.01016-11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ninety-six samples from hepatitis B virus (HBV)-infected individuals were used to compare ViveST samples to frozen samples in COBAS TaqMan, RealArt, and VERSANT. Correlation (r) between ViveST samples and frozen samples was 0.99 in all three platforms. Correlations among tests using frozen samples were 0.96 for COBAS and RealArt, 0.94 for COBAS and VERSANT, and 0.97 for VERSANT and RealArt. The results indicate that ViveST may be useful in clinical practice. Different HBV-VL platforms correlated well with one another.
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Winters M, Lloyd R, Shahidi A, Brown S, Holodniy M. Use of dried clinical samples for storing and detecting influenza RNA. Influenza Other Respir Viruses 2011; 5:413-7. [PMID: 21668673 PMCID: PMC5780658 DOI: 10.1111/j.1750-2659.2011.00253.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Please cite this paper as: Winters et al. (2011) Use of dried clinical samples for storing and detecting influenza RNA. Influenza and Other Respiratory Viruses 5(6), 413–417. Background Most clinical samples collected for diagnostic influenza testing and monitoring require refrigerated or frozen storage or shipment, which imparts logistic and cost burdens. The ability to store and ship dried clinical specimens under ambient conditions for influenza testing would significantly reduce costs and protect samples from improper storage or equipment failure, especially in remote or resource‐limited areas. Objectives To evaluate the collection and storage of dried clinical samples on a transport matrix (ViveST™, ST) for influenza RNA testing by real‐time reverse‐transcription PCR (RT‐PCR). Methods Viral transport medium from swab or sputum samples was applied to ST, dried, and stored under ambient conditions from 2 days to 6 months. Additional aliquots of samples were frozen. Testing of frozen and ST‐stored samples was performed using the WHO/CDC real‐time influenza A (H1N1) RT‐PCR protocol and compared to the Luminex xTAG RVP assay. Results ST‐stored samples yielded slightly higher threshold cycle values (median 2·54 cycles) compared to frozen samples tested in parallel. This difference was consistent regardless of viral input. There was no significant difference in signal recovery between samples stored for 1 week versus samples stored for 3 weeks, or from three samples stored for 6 months. Qualitatively, clinical specimens stored on ST were 100% concordant (36/36) with frozen samples for detecting the presence of influenza A RNA. Conclusion ST‐processed dried specimens produced similar rates of seasonal or novel 2009 HIN1 influenza RNA detection compared to conventional sample processing and thus presents a viable alternative to refrigerated or frozen samples.
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Affiliation(s)
- Mark Winters
- VA Palo Alto Health Care System, Palo Alto, CA, USA.
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Comparative effectiveness of dried plasma HIV-1 viral load testing in Brazil using ViveST for sample collection. J Clin Virol 2010; 49:245-8. [DOI: 10.1016/j.jcv.2010.08.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Revised: 08/20/2010] [Accepted: 08/28/2010] [Indexed: 11/18/2022]
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18
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Patnaik SK, Mallick R, Yendamuri S. Detection of microRNAs in dried serum blots. Anal Biochem 2010; 407:147-9. [PMID: 20696125 DOI: 10.1016/j.ab.2010.08.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 08/02/2010] [Accepted: 08/02/2010] [Indexed: 10/19/2022]
Abstract
We observed the preservation of microRNAs in unrefrigerated dried serum blots. Preservation was not adversely affected by drying or storing at 37, 45, or 60°C instead of room temperature, but it was harmed when blots were dried incompletely before storage. Preservation of microRNAs in serum was not diminished if, instead of being kept frozen at -80°C, it was stored as dried blots at room temperature for 5 months or at 37°C for 4 weeks. Thus, dried blots can be a convenient and safer way to save, transport, and store serum for microRNA assays.
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Affiliation(s)
- Santosh Kumar Patnaik
- Department of Thoracic Surgery, Roswell Park Cancer Institute, Buffalo, NY 14203, USA.
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De Crignis E, Re MC, Cimatti L, Zecchi L, Gibellini D. HIV-1 and HCV detection in dried blood spots by SYBR Green multiplex real-time RT-PCR. J Virol Methods 2010; 165:51-6. [PMID: 20045028 DOI: 10.1016/j.jviromet.2009.12.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2009] [Revised: 12/17/2009] [Accepted: 12/21/2009] [Indexed: 01/12/2023]
Abstract
Dried blood spot (DBS) is a reliable method of blood collection used for the diagnosis of several human diseases. DBS is particularly useful for diagnosing children and for the screening of high-risk populations especially in countries where health facilities are not readily accessible. This report describes a qualitative SYBR Green-based real-time multiplex RT-PCR for the simultaneous detection of hepatitis C virus (HCV) and human immunodeficiency virus type 1 (HIV-1) genomes in DBS. Specific viral amplicons were identified in the same sample by their distinctive melting temperatures. The analysis of scalar concentrations of the reference samples indicated that this multiplex procedure detects at least 2500 copies/ml of HCV and 400 copies/ml of HIV-1. HIV-1 and HCV viral loads in 20 patients infected with HIV-1 and/or HCV and in 5 healthy blood donors were also tested, confirming the sensitivity and specificity of the assay. This method may represent a reliable alternative for the detection of HIV-1/HCV co-infection, in rapid and relatively inexpensive screening programmes.
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Affiliation(s)
- Elisa De Crignis
- Department of Haematology and Oncologic Sciences, Section of Microbiology, Rome, Italy
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